surv_analysis {multiClust} | R Documentation

## Function to produce Kaplan-Meier Survival Plots of selected gene expression data.

### Description

Function to produce Kaplan-Meier Survival Plots of selected gene expression data.

### Usage

    surv_analysis(samp_cluster, clinical, survival_type = "RFS", data_name,
      cluster_type = "HClust", distance = "euclidean",
      linkage_type = "ward.D2", probe_rank = "SD_Rank",
      probe_num_selection = "Fixed_Probe_Num",
      cluster_num_selection = "Fixed_Clust_Num")

### Arguments

`samp_cluster` | Object vector containing the samples and the cluster number they belong to. This object is an output of the cluster_analysis function.
`clinical` | String indicating the name of the text file containing patient clinical information. The file should be a data frame consisting of two columns. The first column contains the patient survival time information in months. The second column indicates occurrence of a censorship (0) or an event (1).
`survival_type` | String specifying the type of survival event being analyzed. Examples include "Disease-free survival (DFS)", "Overall Survival (OS)", "Relapse-free survival (RFS)", etc.
`data_name` | String indicating the name to be used to label the plot.
`cluster_type` | String indicating the type of clustering method used in the cluster_analysis function. "Kmeans" or "HClust" are the two options.
`distance` | String describing the distance metric uses for HClust in the cluster_analysis function. Options include one of "euclidean", "maximum", manhattan", "canberra", "binary", or "minkowski".
`linkage_type` | String describing the linkage metric use in the cluster_analysis function. Options include "ward.D2", "average", "complete", "median", "centroid", "single", and "mcquitty".
`probe_rank` | String indicating the feature selection method used in the probe_ranking function. Options include "CV_Rank", "CV_Guided", "SD_Rank", and "Poly".
`probe_num_selection` | String indicating the way in which probes were selected in the number_probes function. Options include "Fixed_Probe_Num", "Percent_Probe_Num", and "Adaptive_Probee_Num".
`cluster_num_selection` | String indicating how the number of clusters were determined in the number_clusters function. Options include "Fixed_Clust_Num" and "Gap_Statistic".

### Value

Produces a pdf image of a Kaplan-Meier Survival Plot with Cox Survival P Value. Also returns an object containing the cox survival P value.

### Author(s)

Alec Fabbri, Nathan Lawlor

### See Also

`number_clusters`, `number_probes`, `probe_ranking`, `cluster_analysis`, `coxph`

### Examples

    # Load in a data file
    data_file <- system.file("extdata", "GSE2034.normalized.expression.txt",
        package="multiClust")
    data <- input_file(input=data_file)
    # Choose 300 genes to select for
    gene_num <- number_probes(input=data_file, data.exp=data, Fixed=300,
        Percent=NULL, Adaptive=NULL)
    # Choose the "CV_Rank" Method for gene ranking
    sel.data <- probe_ranking(input=data_file, probe_number=300,
        probe_num_selection="Fixed_Probe_Num", data.exp=data, method="CV_Rank")
    # Choose a fixed cluster number of 3
    clust_num <- number_clusters(data.exp=data, Fixed=3, gap_statistic=NULL)
    # Call function for Kmeans parameters
    kmeans_analysis <- cluster_analysis(sel.exp=sel.data, cluster_type="Kmeans",
        distance=NULL, linkage_type=NULL, gene_distance=NULL,
        num_clusters=3, data_name="GSE2034 Breast",
        probe_rank="CV_Rank", probe_num_selection="Fixed_Probe_Num",
        cluster_num_selection="Fixed_Clust_Num")
    # Load the clinical outcome file
    clin_file <- system.file("extdata", "GSE2034-RFS-clinical-outcome.txt",
        package="multiClust")
    # Example of Calling surv_analysis function
    surv <- surv_analysis(samp_cluster=kmeans_analysis, clinical=clin_file,
        survival_type="RFS", data_name="GSE2034 Breast", cluster_type="Kmeans",
         distance=NULL, linkage_type=NULL, probe_rank="CV_Rank",
         probe_num_selection="Fixed_Probe_Num",
         cluster_num_selection="Fixed_Cluster_Num")

[Package multiClust version 1.17.0 Index]